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1.
Diagn Microbiol Infect Dis ; 99(1): 115206, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1023529

ABSTRACT

The diagnosis of coronavirus disease-19 (COVID-19) relies on the detection of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) RNA by real-time reverse-transcription polymerase chain reaction in respiratory samples. Rapid increase in the COVID-19 cases across the world requires fast and efficient testing as testing capacity is a bottleneck in diagnosis. In this context, pooling strategy can be opted for rapid testing in a cost-effective manner. In this study, the authors have optimized and compared the effect of pooling (5 and 10 samples) before and after nucleic acid extraction. It was concluded that there was no significant difference in the SARS CoV-2 RNA detection in the pools prepared at sample or RNA level. Even after pooling, 10-fold dilution was detectable with 3-cycle threshold value change in both type of pools when compared with individual samples. Hence, sample pool size of 10 can be used in low-prevalent areas, and testing capacity can be substantially increased.


Subject(s)
/methods , /isolation & purification , Specimen Handling/methods , /standards , Genes, Viral/genetics , Humans , India/epidemiology , Nasopharynx/virology , Pharynx/virology , RNA, Viral/genetics , RNA, Viral/isolation & purification , Sensitivity and Specificity , Specimen Handling/standards , Tertiary Care Centers
2.
J Virol Methods ; 289: 114044, 2021 03.
Article in English | MEDLINE | ID: covidwho-971001

ABSTRACT

The worldwide COVID-19 pandemic outburst has caused a serious public health issue with increasing needs of accurate and rapid diagnostic and screening testing. This situation requires an optimized management of the chemical reagents, the consumables, and the human resources, in order to respond accurately and effectively, controlling the spread of the disease. Testing on pooled samples maximizes the number of tested samples, by minimizing the time and the lab supplies needed. The general conceptualization of the pooling method is based on mixing samples together in a batch. Individual testing is needed only if a specific pool exhibits a positive result. The development of alternative hybrid methods, based on "in house" protocols, utilizing commercially available consumables, in combination with a reliable pooling method would provide a solution, focusing on the better exploitation of the personnel and the lab supplies, allowing for rapid screening of a population in a reasonably short time.


Subject(s)
/diagnosis , Specimen Handling/methods , /epidemiology , Diagnostic Tests, Routine , Humans , Pandemics , Specimen Handling/standards
3.
Viruses ; 12(11)2020 10 23.
Article in English | MEDLINE | ID: covidwho-895403

ABSTRACT

Critical to facilitating SARS-CoV-2 point-of-care (POC) testing is assurance that viruses present in specimens are inactivated onsite prior to processing. Here, we conducted experiments to determine the virucidal activity of commercially available Viral Transport Mediums (VTMs) to inactivate SARS-CoV-2. Independent testing methods for viral inactivation testing were applied, including a previously described World Health Organization (WHO) protocol, in addition to a buffer exchange method where the virus is physically separated from the VTM post exposure. The latter method enables sensitive detection of viral viability at higher viral titre when incubated with VTM. We demonstrate that VTM formulations, Primestore® Molecular Transport Medium (MTM) and COPAN eNAT™ completely inactivate high-titre SARS-CoV-2 virus (>1 × 107 copies/mL) and are compatible with POC processing. Furthermore, full viral inactivation was rapidly achieved in as little as 2 min of VTM exposure. We conclude that adding certain VTM formulations as a first step post specimen collection will render SARS-CoV-2 non-infectious for transport, or for further in-field POC molecular testing using rapid turnaround GeneXpert platforms or equivalent.


Subject(s)
Betacoronavirus/isolation & purification , Point-of-Care Testing , Specimen Handling , Virus Inactivation , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Culture Media/analysis , Culture Media/pharmacology , Humans , Point-of-Care Testing/standards , Specimen Handling/methods , Specimen Handling/standards , Viral Load/drug effects , Virus Inactivation/drug effects
7.
J Forensic Leg Med ; 76: 102067, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-863228

ABSTRACT

On 31 December 2019, health authorities in the People's Republic of China informed the World Health Organization of a then limited outbreak of interstitial viral pneumonia, identified at a laboratory in the city of Wuhan. In mid-April 2020 this outbreak of COVID-19 (as the disease has been called) has aggravated and spread worldwide, causing more than 200,000 deaths and affecting especially the United States, Spain, Italy, France and the United Kingdom. Despite the severity of the outbreak, the pathological findings have not been described in detail and there are very few guidelines or protocols for conducting autopsy studies on patients who have died from COVID-19. There are currently very few histopathological case series studies on this disease. In addition, some of these studies have been performed on biopsies or surgical resection pieces from patients in whom disease was subsequently demonstrated or through minimally invasive autopsy protocols. None of the studies offer a detailed necropsy protocol. This document proposes a protocol of action for the institutes of Forensic Medicine facing the current SARS-CoV2 pandemic, which combines protection of worker safety with optimization of tissue collection.


Subject(s)
Betacoronavirus , Coronavirus Infections/pathology , Forensic Pathology/standards , Pneumonia, Viral/pathology , Practice Guidelines as Topic , Specimen Handling/standards , Autopsy , Forensic Medicine/standards , Forensic Sciences/standards , Humans , Pandemics
8.
J Forensic Leg Med ; 76: 102067, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-813686

ABSTRACT

On 31 December 2019, health authorities in the People's Republic of China informed the World Health Organization of a then limited outbreak of interstitial viral pneumonia, identified at a laboratory in the city of Wuhan. In mid-April 2020 this outbreak of COVID-19 (as the disease has been called) has aggravated and spread worldwide, causing more than 200,000 deaths and affecting especially the United States, Spain, Italy, France and the United Kingdom. Despite the severity of the outbreak, the pathological findings have not been described in detail and there are very few guidelines or protocols for conducting autopsy studies on patients who have died from COVID-19. There are currently very few histopathological case series studies on this disease. In addition, some of these studies have been performed on biopsies or surgical resection pieces from patients in whom disease was subsequently demonstrated or through minimally invasive autopsy protocols. None of the studies offer a detailed necropsy protocol. This document proposes a protocol of action for the institutes of Forensic Medicine facing the current SARS-CoV2 pandemic, which combines protection of worker safety with optimization of tissue collection.


Subject(s)
Betacoronavirus , Coronavirus Infections/pathology , Forensic Pathology/standards , Pneumonia, Viral/pathology , Practice Guidelines as Topic , Specimen Handling/standards , Autopsy , Forensic Medicine/standards , Forensic Sciences/standards , Humans , Pandemics
9.
J Mol Diagn ; 22(10): 1294-1299, 2020 10.
Article in English | MEDLINE | ID: covidwho-802774

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing has lagged in many countries because of test kit shortages and analytical process bottlenecks. This study investigated the feasibility and accuracy of a sample pooling approach for wide-scale population screening for coronavirus disease 2019. A total of 940 nasopharyngeal swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were deidentified and assigned random numbers for analysis, and 94 pools of 10 samples each were generated. Automated RNA extraction, followed by RT-PCR, was performed in a 96-well plate. Positive pools were identified, and the individual samples were reanalyzed. Of the 94 pools/wells, four were positive [Ct values: N (22.7 to 28.3), ORF1ab (23.3 to 27.2), and internal control (34.4 to 35.4)]. The 40 samples comprising the four pools were identified and reanalyzed individually; six samples were positive, with Ct values of N gene, ORF1ab, and internal control comparable to their respective wells. Additional experiments were performed on samples with high Ct values, and overall results showed 91.6% positive and 100% negative agreement compared with individual testing approach. Thus, 940 samples were tested in 148 reactions compared with 940 reactions in routine screening. The sample pooling strategy may help catch up with testing needs and minimal turnaround times and facilitate enormous savings on laboratory supplies, extraction, and PCR kits currently in short supply.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Diagnostic Tests, Routine/methods , Mass Screening/methods , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , Specimen Handling/standards , Betacoronavirus/isolation & purification , Coronavirus Infections/genetics , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction
10.
Arch Pathol Lab Med ; 144(9): 1048-1056, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-771248

ABSTRACT

CONTEXT.­: The novel coronavirus disease 2019 (COVID-19) pandemic is significantly changing methodologic approaches in all branches of the health system. From a forensic point of view, this event is partly changing the manner in which forensic pathologists and all those who work in autopsy services operate, but above all, it is changing the patterns established for years by which cadavers are analyzed postmortem. OBJECTIVE.­: To present a review of the literature and a proposal for COVID-19 autopsy protocols. To contain the infection risk, a revision of all the protocols that until now have been applied to the examination of bodies that require autopsy services is required. DATA SOURCES.­: Currently, the diagnosis and postmortem analysis of positive or suspected COVID-19 cases plays a crucial role in scientific research. A review of the main recommendations proposed by international scientific societies regarding the risk of infection during autopsy was carried out. Scientific papers currently available via the PubMed NCBI search engine on COVID-19 postmortem diagnosis were also examined. CONCLUSIONS.­: Throughout the history of medicine, autopsy has been fundamental to the understanding of multiple pathogenic processes that are investigated postmortem. The purpose of the study is to propose an operating protocol that can be useful for all clinical and forensic autopsies, with particular reference to the correct methods to be applied to the examination of positive or suspected COVID-19 cases, regarding both the autopsy procedure and the collection and analysis of biological samples.


Subject(s)
Autopsy/methods , Betacoronavirus , Coronavirus Infections/prevention & control , Infection Control/methods , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Autopsy/standards , Coronavirus Infections/diagnosis , Coronavirus Infections/pathology , Coronavirus Infections/transmission , Humans , Infection Control/standards , Pneumonia, Viral/diagnosis , Pneumonia, Viral/pathology , Pneumonia, Viral/transmission , Risk Assessment , Specimen Handling/methods , Specimen Handling/standards
11.
Clin Chim Acta ; 510: 717-722, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-764338

ABSTRACT

AIM: This study aims to verify whether standardized saliva collection is suitable for SARS-CoV-2 molecular detection and IgA measurement. METHODS: 43 COVID-19 inpatients and 326 screening subjects underwent naso-pharyngeal (NP)-swab and saliva collection (Salivette). Inpatients also underwent repeated blood collections to evaluate inflammation and organs involvement. In all patients and subjects, SARS-CoV-2 (gene E) rRT-PCR was undertaken in saliva and NP-swabs. Salivary IgA and serum IgA, IgG, IgM were measured on inpatients' samples. RESULTS: NP-swabs and saliva were both SARS-CoV-2 positive in 7 (16%) or both negative in 35 (82%) out of 43 patients successfully included in the study. NP-swabs and saliva results did not perfectly match in one patient (saliva positive, NP-swab negative). Positive molecular results were significantly associated with disease duration (p = 0.0049). 326/326 screening subjects were SARS-CoV-2 negative on both NP-swabs and saliva. Among the 27 saliva samples tested for IgA, 18 were IgA positive. Salivary IgA positivity was associated with pneumonia (p = 0.002) and CRP values (p = 0.0183), not with other clinical and molecular data, or with serum immunoglubulins. CONCLUSIONS: A standardized saliva collection can be adopted to detect SARS-CoV-2 infection in alternative to NP-swabs. Preliminary data on salivary IgA support the use of saliva also for patient monitoring.


Subject(s)
Betacoronavirus/immunology , Clinical Laboratory Techniques , Immunoglobulin A/analysis , Saliva/chemistry , Specimen Handling/standards , Adult , Aged , Aged, 80 and over , Coronavirus Infections/diagnosis , Female , Humans , Immunoglobulin A/immunology , Male , Middle Aged , Reference Standards
12.
Indian J Gastroenterol ; 39(3): 236-242, 2020 06.
Article in English | MEDLINE | ID: covidwho-739687

ABSTRACT

The outbreak of Corona Virus Disease-19 (COVID-19), caused by Severe Acute Respiratory Syndrome Corona Virus - 2 (SARS-CoV-2), a global pandemic, is having a significant impact on healthcare, especially the clinical microbiology laboratories all around the world. There are many reports which suggest that the disease can present with gastrointestinal symptoms such as nausea, vomiting, diarrhea, and loss of appetite, which the gastroenterologists may have to deal with. Hence, knowledge about the diagnosis of COVID-19 is important to gastroenterologists as well. The current review therefore covers the challenges faced while choosing appropriate sample collection, transport, and tests for SARS-CoV-2 infection. The right sample at the right time from the right anatomical site with the proper precautions is crucial in prompt and accurate diagnosis of COVID-19. The tests can be divided into direct, indirect, and complementary tests. In the direct test, real-time polymerase chain reaction (RT-PCR) assays are the molecular tests of choice for the diagnosis of COVID-19. Other direct tests include GeneXpert and TrueNAT. In indirect testing, antigen-antibody-based techniques are recommended for surveillance for the disease, which may help to formulate the control measures. Finally, the additional tests help in assessing the disease severity and evaluating the prognosis. All the above tests are important not only for diagnosis but also for management strategy and prognosis.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections , Pandemics , Pneumonia, Viral , Clinical Laboratory Techniques/standards , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Prognosis , Reproducibility of Results , Specimen Handling/methods , Specimen Handling/standards
13.
Endocrine ; 70(3): 454-460, 2020 12.
Article in English | MEDLINE | ID: covidwho-737716

ABSTRACT

PURPOSE: The length of time a critically ill coronavirus disease 2019 (COVID-19) patient remains infectious and should therefore be isolated remains unknown. This prospective study was undertaken in critically ill patients to evaluate the reliability of single negative real-time polymerase chain reaction (RT-PCR) in lower tracheal aspirates (LTA) in predicting a second negative test and to analyze clinical factors potentially influencing the viral shedding. METHODS: From April 9, 2020 onwards, intubated COVID-19 patients treated in the intensive care unit were systematically evaluated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR of nasopharyngeal swabs and LTA. The time to negativity was defined as the time between the onset of symptoms and the viral clearance in LTA. In order to identify risk factors for prolonged viral shedding, we used univariate and multivariate Cox proportional hazards models. RESULTS: Forty-eight intubated SARS-CoV-2 patients were enrolled. Overall, we observed that the association of the first negative RT-PCR with a second negative result was 96.7%. Median viral shedding was 25 (IQR: 21.5-28) days since symptoms' onset. In the univariate Cox model analysis, type 2 diabetes mellitus was associated with a prolonged viral RNA shedding (hazard ratio [HR]: 0.41, 95% CI: 0.06-3.11, p = 0.04). In the multivariate Cox model analysis, type 2 diabetes was associated with a prolonged viral RNA shedding (HR: 0.31, 95% CI: 0.11-0.89, p = 0.029). CONCLUSION: Intubated patients with type 2 diabetes mellitus may have prolonged SARS-CoV-2 shedding. In critically ill COVID-19 patients, one negative LTA should be sufficient to assess and exclude infectivity.


Subject(s)
Betacoronavirus/physiology , Coronavirus Infections/virology , Critical Illness , Diabetes Mellitus, Type 2/virology , Pneumonia, Viral/virology , Respiratory System/virology , Virus Shedding , Aged , Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Comorbidity , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/epidemiology , Disease Progression , Female , Humans , Intensive Care Units , Italy/epidemiology , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Predictive Value of Tests , Prognosis , Prospective Studies , Reproducibility of Results , Respiratory System/pathology , Reverse Transcriptase Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/standards , Risk Factors , Specimen Handling/methods , Specimen Handling/standards , Switzerland/epidemiology , Time Factors
14.
Crit Care Med ; 48(11): 1680-1689, 2020 11.
Article in English | MEDLINE | ID: covidwho-725707

ABSTRACT

OBJECTIVES: We explore ways to reduce errors in laboratory diagnosis of severe acute respiratory syndrome-coronavirus 2 infection by considering preanalytic, analytic, and postanalytic sources. To address preanalytic challenges, we first consider alternative anatomic sites for specimen collection, then discuss self-collection, alternative sampling devices, and transport media. Strengths and limitations of various analytic test systems are considered in the context of postanalytic challenges associated with making test results meaningful, specifically considering the complex relationship between "positive" test results and reproduction and shedding of intact virus. Finally, we provide recommendations regarding healthcare worker surveillance and release of patients with coronavirus disease 2019 from isolation. DATA SOURCES: Material was derived from a Webinar available to the public, manufacturer's websites, U.S. Food and Drug Administration, and Centers for Disease Control and Prevention websites and from both peer-reviewed papers identified by PubMed search and nonpeer-reviewed papers posted on Biorxiv and Medrxiv. Unpublished data came from the Washington State Department of Health. STUDY SELECTION: We included studies that compared diagnostic performance strategies without introducing bias due to use of an imperfect gold standard. Case series and case reports were included as necessary to illuminate the significance of results. DATA EXTRACTION: Data were extracted manually. DATA SYNTHESIS: Sensitivity, specificity, and CIs were computed from article data using a composite reference standard. Nucleic acid-based tests were assumed to perform at 100% specificity. CONCLUSIONS: Although sputum and bronchoalveolar lavage samples provide the highest diagnostic sensitivity for severe acute respiratory syndrome-coronavirus 2, nasopharyngeal, mid turbinate, and nasal specimens are suitable in most cases and require less use of personal protective equipment. When desired sampling materials are unavailable, alternatives may be substituted with no loss of performance. Both reverse transcriptase polymerase chain reaction tests and rapid nucleic acid-based tests offer good performance in most circumstances. Testing is not required to release most patients from isolation.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Specimen Handling/standards , Centers for Disease Control and Prevention, U.S. , Clinical Laboratory Techniques , Humans , Pandemics , Reverse Transcriptase Polymerase Chain Reaction , United States
15.
Curr Microbiol ; 77(11): 3680-3684, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-722253

ABSTRACT

Thorough swabbing is becoming an increasing approach to fight COVID-19 transmission, particularly among asymptomatic subjects, who are thought to represent the majority of potentially-contacting people. Particularly in the current management of COVID-19 emergency, the 3T approach, i.e., testing, tracing and treating, is felt as particularly crucial to fight COVID-19 pandemic. Aside from the time-consuming, cost expensive and the many burdensome issues associated with a thorough swabbing, adopting easy-to-make criteria such as "drive-thru-swab" may exacerbate the burden of critical biases and pre-analytical errors, which may impair the analytical reliability of these tests. This manuscript addresses some major points about.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , Betacoronavirus/pathogenicity , Biomarkers/analysis , Contact Tracing/statistics & numerical data , Coronavirus Infections/transmission , Coronavirus Infections/virology , False Negative Reactions , Hospitalization , Humans , Italy/epidemiology , Personal Protective Equipment/supply & distribution , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction , Specimen Handling/standards
17.
Biochem Med (Zagreb) ; 30(3): 030503, 2020 Oct 15.
Article in English | MEDLINE | ID: covidwho-710277

ABSTRACT

The new corona virus SARS-CoV-2 (Severe Acute Respiratory Syndrome Corona Virus 2) causes a disease called COVID-19 (coronavirus disease 2019), that develops mostly in subjects with already impaired immune system function, primarily in the elderly and in individuals with some chronic disease or condition. The reasons for this should be sought in the processes of aging and chronic latent inflammation, i.e. immunosenescence and inflammaging. Laboratory medicine specialists are currently focused on proving the presence of the virus and defining biomarkers that would enable the prediction of disease progression. For now, it has been shown that useful biomarkers can include general biomarkers of inflammation (parameters of complete blood count, C-reactive protein, interleukin-6, procalcitonin), biomarkers of myocardial damage (high sensitivity troponin I/T, B-type natriuretic peptide, and N-terminal B type natriuretic peptide), and vascular biomarkers (D-dimer, prothrombin time, fibrinogen). Their actual diagnostic specificity, sensitivity and predictive value need to be tested on a larger number of subjects. In addition, it is important to find and evaluate specific biomarkers of immunosenescence.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/standards , Coronavirus Infections/blood , Health Personnel/standards , Inflammation Mediators/blood , Pneumonia, Viral/blood , Specimen Handling/standards , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/metabolism , Humans , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/metabolism , Specimen Handling/methods
18.
J Virol Methods ; 285: 113947, 2020 11.
Article in English | MEDLINE | ID: covidwho-695693

ABSTRACT

On March 11, 2020, the World Health Organization (WHO) assessed COVID-19, caused by SARS-CoV-2, as a pandemic. As of June 1, 2020, SARS-CoV-2 has had a documented effect of over 6 million cases world-wide, amounting to over 370,000 deaths (World Health Organization, 2020. Novel Coronavirus (COVID-19) Situation. http://https://covid19.who.int/). Consequently, the high demand for testing has resulted in a depletion of commercially available consumables, including the recommended swabs and viral transport media (VTM) required for nasopharyngeal sampling. Therefore, the potential use of unvalidated alternatives must be explored to address the global shortage of testing supplies. To tackle this issue, we evaluated the utility of different swabs and transport mediums for the molecular detection of SARS-CoV-2. This study compared the performance of six swabs commonly found in primary and tertiary health care settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima) for their efficacy in testing for SARS-CoV-2. Separately, the molecular detection of SARS-CoV-2 was completed from different transport mediums (DMEM, PBS, 100 % ethanol, 0.9 % normal saline and VTM), which were kept up to three days at room temperature (RT). The results indicate that there is no meaningful difference in viral yield from different swabs and most transport mediums for the collection and detection of SARS-CoV-2, indicating swab and medium alternatives could be used if supplies run out.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Coronavirus Infections/epidemiology , Humans , Pandemics , Pneumonia, Viral/epidemiology , Reproducibility of Results , Specimen Handling/methods , Specimen Handling/standards
19.
J Mol Diagn ; 22(10): 1294-1299, 2020 10.
Article in English | MEDLINE | ID: covidwho-691053

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing has lagged in many countries because of test kit shortages and analytical process bottlenecks. This study investigated the feasibility and accuracy of a sample pooling approach for wide-scale population screening for coronavirus disease 2019. A total of 940 nasopharyngeal swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were deidentified and assigned random numbers for analysis, and 94 pools of 10 samples each were generated. Automated RNA extraction, followed by RT-PCR, was performed in a 96-well plate. Positive pools were identified, and the individual samples were reanalyzed. Of the 94 pools/wells, four were positive [Ct values: N (22.7 to 28.3), ORF1ab (23.3 to 27.2), and internal control (34.4 to 35.4)]. The 40 samples comprising the four pools were identified and reanalyzed individually; six samples were positive, with Ct values of N gene, ORF1ab, and internal control comparable to their respective wells. Additional experiments were performed on samples with high Ct values, and overall results showed 91.6% positive and 100% negative agreement compared with individual testing approach. Thus, 940 samples were tested in 148 reactions compared with 940 reactions in routine screening. The sample pooling strategy may help catch up with testing needs and minimal turnaround times and facilitate enormous savings on laboratory supplies, extraction, and PCR kits currently in short supply.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Diagnostic Tests, Routine/methods , Mass Screening/methods , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , Specimen Handling/standards , Betacoronavirus/isolation & purification , Coronavirus Infections/genetics , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction
20.
Lancet Infect Dis ; 20(10): e268-e273, 2020 10.
Article in English | MEDLINE | ID: covidwho-671309

ABSTRACT

Outbreaks of infectious diseases are occurring with increasing frequency and unpredictability. The rapid development and deployment of diagnostics that can accurately and quickly identify pathogens as part of epidemic preparedness is needed now for the COVID-19 pandemic. WHO has developed a global research and innovation forum to facilitate, accelerate, and deepen research collaboration among countries and funders. Great progress has been made in the past decade, but access to specimens remains a major barrier for the development and evaluation of needed quality diagnostics. We present a sustainable model for a global network of country-owned biobanks with standardised methods for collection, characterisation, and archiving of specimens and pathogens to facilitate and accelerate diagnostics development and evaluation for COVID-19 and other diseases of epidemic potential. The biobanking network should be run on the guiding principles of transparency, equitable access, ethics, and respect for national laws that support country ownership and sustainability. Adapting the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits, sharing of specimens from national biobanks can be rewarded through mechanisms such as equitable access to diagnostics at negotiated prices. Such networks should be prepared for any pathogen of epidemic potential.


Subject(s)
Biological Specimen Banks/organization & administration , Biological Specimen Banks/standards , Communicable Diseases/diagnosis , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus/isolation & purification , Communicable Disease Control , Communicable Diseases/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Diagnostic Tests, Routine , Epidemics/prevention & control , Humans , International Cooperation , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Specimen Handling/standards , Sustainable Development
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